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Abstract:

The ubiquitous heme proteins perform a wide variety of tasks that rely on the subtle regulation of their affinity for small ligands like O2, CO, and NO. Ligand affinity is characterized by kinetic association and dissociation rate constants, that partially depend on ligand migration between the solvent and active site, mediated by the presence of internal cavities or tunnels. Different computational methods have been developed to study these processes which can be roughly divided in two strategies: those costly methods in which the ligand is treated explicitly during the simulations, and the free energy landscape of the process is computed; and those faster methods that use prior computed Molecular Dynamics simulation without the ligand, and incorporate it afterwards, called implicit ligand sampling (ILS) methods. To compare both approaches performance and to provide a combined protocol to study ligand migration in heme proteins, we performed ILS and multiple steered molecular dynamics (MSMD) free energy calculations of the ligand migration process in three representative and well theoretically and experimentally studied cases that cover a wide range of complex situations presenting a challenging benchmark for the aim of the present work. Our results show that ILS provides a good description of the tunnel topology and a reasonable approximation to the free energy landscape, while MSMD provides more accurate and detailed free energy profile description of each tunnel. Based on these results, a combined strategy is presented for the study of internal ligand migration in heme proteins. © 2011 Wiley Periodicals, Inc.

Registro:

Documento: Artículo
Título:Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins
Autor:Forti, F.; Boechi, L.; Estrin, D.A.; Marti, M.A.
Filiación:Department de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
Departamento de Química Biolõgica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:AMBER; cavities; CO; docking sites; free energy profile; ILS; implicit ligand sampling; ligand migration; MD; molecular dynamics; MSMD; multiple steered molecular dynamics; nitrophorin; NO; O2; proteins; truncated haemoglobin; tunnels; xenon sites; cavities; docking sites; free energy profile; Haemoglobins; ILS; implicit ligand sampling; MSMD; Nitrophorin; Steered molecular dynamics; Dissociation; Dynamics; Free energy; Ligands; Molecular dynamics; Porphyrins; Rate constants; Proteins; carbon monoxide; hemoprotein; ligand; nitric oxide; oxygen; chemistry; kinetics; molecular dynamics; thermodynamics; Carbon Monoxide; Hemeproteins; Kinetics; Ligands; Molecular Dynamics Simulation; Nitric Oxide; Oxygen; Thermodynamics
Año:2011
Volumen:32
Número:10
Página de inicio:2219
Página de fin:2231
DOI: http://dx.doi.org/10.1002/jcc.21805
Título revista:Journal of Computational Chemistry
Título revista abreviado:J. Comput. Chem.
ISSN:01928651
CODEN:JCCHD
CAS:carbon monoxide, 630-08-0; nitric oxide, 10102-43-9; oxygen, 7782-44-7; Carbon Monoxide; Hemeproteins; Ligands; Nitric Oxide; Oxygen
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v32_n10_p2219_Forti

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Citas:

---------- APA ----------
Forti, F., Boechi, L., Estrin, D.A. & Marti, M.A. (2011) . Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. Journal of Computational Chemistry, 32(10), 2219-2231.
http://dx.doi.org/10.1002/jcc.21805
---------- CHICAGO ----------
Forti, F., Boechi, L., Estrin, D.A., Marti, M.A. "Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins" . Journal of Computational Chemistry 32, no. 10 (2011) : 2219-2231.
http://dx.doi.org/10.1002/jcc.21805
---------- MLA ----------
Forti, F., Boechi, L., Estrin, D.A., Marti, M.A. "Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins" . Journal of Computational Chemistry, vol. 32, no. 10, 2011, pp. 2219-2231.
http://dx.doi.org/10.1002/jcc.21805
---------- VANCOUVER ----------
Forti, F., Boechi, L., Estrin, D.A., Marti, M.A. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. J. Comput. Chem. 2011;32(10):2219-2231.
http://dx.doi.org/10.1002/jcc.21805